Immune evasion by varicelloviruses : the identification of a new family of TAP-inhibiting proteins

From the earliest times of their evolution, multi-cellular organisms have been defending themselves against infectious agents like nucleic acids, viruses, bacteria, fungi and parasites. Continuous selection pressure resulted in the development of sophisticated immune systems, which in their adaptive forms have exquisite specificity as well as memory for pathogen antigens. On the other hand, infectious agents developed elaborate strategies to escape from, or counteract, host defense mechanisms. Viruses are totally dependent upon host cells for replication and have developed an impressive variety of mechanisms to shield themselves from being detected by the host immune system. The subject of this thesis concerns a particular example of how viruses, specifically some members of genus Varicellovirus, counteract an important step in one of the acquired immunity pathways: the presentation of antigen by Major Histocompatibility Complex (MHC) class I molecules to cytotoxic T-cells. This thesis describes the discovery of a new family of proteins that inhibit the Transporter associated with Antigen Processing (TAP), and sets the first steps towards the explanation of how these inhibitors interfere with antigen transport by the MHC class I loading complex.Department of Medical MicrobiologyUBL - phd migration 201

DeepTract: A Probabilistic Deep Learning Framework for White Matter Fiber Tractography

We present DeepTract, a deep-learning framework for estimating white matter fibers orientation and streamline tractography. We adopt a data-driven approach for fiber reconstruction from diffusion weighted images (DWI), which does not assume a specific diffusion model. We use a recurrent neural network for mapping sequences of DWI values into probabilistic fiber orientation distributions. Based on these estimations, our model facilitates both deterministic and probabilistic streamline tractography. We quantitatively evaluate our method using the Tractometer tool, demonstrating competitive performance with state-of-the art classical and machine learning based tractography algorithms. We further present qualitative results of bundle-specific probabilistic tractography obtained using our method. The code is publicly available at: https://github.com/itaybenou/DeepTract.git

Geochemical evidence in the northeast Lau Basin for subduction of the Cook-Austral volcanic chain in the Tonga Trench

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 17 (2016): 1694–1724, doi:10.1002/2015GC006237.Lau Basin basalts host an array of geochemical signatures that suggest incorporation of enriched mantle source material often associated with intraplate hotspots, but the origin of these signatures remain uncertain. Geochemical signatures associated with mantle material entrained from the nearby Samoan hotspot are present in northwest Lau Basin lavas, and subducted seamounts from the Louisville hotspot track may contribute geochemical signatures to the Tonga Arc. However, lavas in the northeast Lau Basin (NELB) have unique enriched geochemical signatures that cannot be related to these hotspots, but can be attributed to the subduction of seamounts associated with the Cook-Austral volcanic lineament. Here we present geochemical data on a new suite of NELB lavas—ranging in 40Ar/39Ar age from 1.3 Ma to 0.365 ka—that have extreme signatures of geochemical enrichment, including lavas with the highest 206Pb/204Pb (19.580) and among the lowest 143Nd/144Nd (0.512697) encountered in the Lau Basin to date. These signatures are linked to the canonical EM1 (enriched mantle 1) and HIMU (high-μ = 238U/204Pb) mantle end-members, respectively. Using a plate reconstruction model, we show that older portions of the traces of two of the Cook-Austral hotspots that contributed volcanism to the Cook-Austral volcanic lineament—the Rarotonga and Rurutu hotspots—were potentially subducted in the Tonga Trench beneath the NELB. The geochemical signatures of the Rarotonga, Rurutu, and Samoan hotspots provide a compelling match to the extreme geochemical components observed in the new NELB lavas.NSF. Grant Number OCE-1153894, EAR-1347377, EAR-1145202, and EAR-1348082; French Agence Nationale de la Recherche Grant Number: ANR-10-BLANC-0603; NSF Grant Numbers: OCE-1154070, OCE-1232985, OCE-1153959 and OCE-14330972016-11-1

Protein Complexes in Urine Interfere with Extracellular Vesicle Biomarker Studies

Urine exosomes (extracellular vesicles; EVs) contain (micro)RNA (miRNA) and protein biomarkers that are useful for the non-invasive diagnosis of various urological diseases. However, the urinary Tamm-Horsfall protein (THP) complex, which forms at reduced temperatures, may affect EV isolation and may also lead to contamination by other molecules including microRNAs (miRNAs). Therefore, we compared the levels of three miRNAs within the purified EV fraction and THP- protein-network. Urine was collected from healthy donors and EVs were isolated by ultracentrifugation (UC), two commercial kits or sepharose size-exclusion chromatography (SEC). SEC enables the separation of EVs from protein-complexes in urine. After UC, the isolation of EV-miRNA was compared with two commercial kits. The EV isolation efficiency was evaluated by measuring the EV protein markers, Alix and TSG101, CD63 by Western blotting, or miR-375, miR-204 and miR-21 by RT-qPCR. By using commercial kits, EV isolation resulted in either low yields or dissimilar miRNA levels. Via SEC, the EVs were separated from the protein-complex fraction. Importantly, a different ratio was observed between the three miRNAs in the protein fraction compared to the EV fraction. Thus, protein-complexes within urine may influence EV-biomarker studies. Therefore, the characterization of the isolated EV fraction is important to obtain reproducible results

Varicellovirus UL 49.5 proteins differentially affect the function of the transporter associated with antigen processing, TAP

Cytotoxic T-lymphocytes play an important role in the protection against viral infections, which they detect through the recognition of virus-derived peptides, presented in the context of MHC class I molecules at the surface of the infected cell. The transporter associated with antigen processing (TAP) plays an essential role in MHC class I–restricted antigen presentation, as TAP imports peptides into the ER, where peptide loading of MHC class I molecules takes place. In this study, the UL49.5 proteins of the varicelloviruses bovine herpesvirus 1 (BHV-1), pseudorabies virus (PRV), and equine herpesvirus 1 and 4 (EHV-1 and EHV-4) are characterized as members of a novel class of viral immune evasion proteins. These UL49.5 proteins interfere with MHC class I antigen presentation by blocking the supply of antigenic peptides through inhibition of TAP. BHV-1, PRV, and EHV-1 recombinant viruses lacking UL49.5 no longer interfere with peptide transport. Combined with the observation that the individually expressed UL49.5 proteins block TAP as well, these data indicate that UL49.5 is the viral factor that is both necessary and sufficient to abolish TAP function during productive infection by these viruses. The mechanisms through which the UL49.5 proteins of BHV-1, PRV, EHV-1, and EHV-4 block TAP exhibit surprising diversity. BHV-1 UL49.5 targets TAP for proteasomal degradation, whereas EHV-1 and EHV-4 UL49.5 interfere with the binding of ATP to TAP. In contrast, TAP stability and ATP recruitment are not affected by PRV UL49.5, although it has the capacity to arrest the peptide transporter in a translocation-incompetent state, a property shared with the BHV-1 and EHV-1 UL49.5. Taken together, these results classify the UL49.5 gene products of BHV-1, PRV, EHV-1, and EHV-4 as members of a novel family of viral immune evasion proteins, inhibiting TAP through a variety of mechanisms

Bovine Herpesvirus Type 1 (BHV-1) UL49.5 Luminal Domain Residues 30 to 32 Are Critical for MHC-I Down-Regulation in Virus-Infected Cells

Bovine herpesvirus type 1 (BHV-1) UL49.5 inhibits transporter associated with antigen processing (TAP) and down-regulates cell-surface expression of major histocompatibility complex (MHC) class I molecules to promote immune evasion. We have constructed a BHV-1 UL49.5 cytoplasmic tail (CT) null and several UL49.5 luminal domain mutants in the backbone of wild-type BHV-1 or BHV-1 UL49.5 CT- null viruses and determined their relative TAP mediated peptide transport inhibition and MHC-1 down-regulation properties compared with BHV-1 wt. Based on our results, the UL49.5 luminal domain residues 30–32 and UL49.5 CT residues, together, promote efficient TAP inhibition and MHC-I down-regulation functions. In vitro, BHV-1 UL49.5 Δ30–32 CT-null virus growth property was similar to that of BHV-1 wt and like the wt UL49.5, the mutant UL49.5 was incorporated in the virion envelope and it formed a complex with gM in the infected cells

A CD8+ T cell immune evasion protein specific to Epstein-Barr virus and its close relatives in Old World primates

γ1-Herpesviruses such as Epstein-Barr virus (EBV) have a unique ability to amplify virus loads in vivo through latent growth-transforming infection. Whether they, like α- and β-herpesviruses, have been driven to actively evade immune detection of replicative (lytic) infection remains a moot point. We were prompted to readdress this question by recent work (Pudney, V.A., A.M. Leese, A.B. Rickinson, and A.D. Hislop. 2005. J. Exp. Med. 201:349–360; Ressing, M.E., S.E. Keating, D. van Leeuwen, D. Koppers-Lalic, I.Y. Pappworth, E.J.H.J. Wiertz, and M. Rowe. 2005. J. Immunol. 174:6829–6838) showing that, as EBV-infected cells move through the lytic cycle, their susceptibility to EBV-specific CD8+ T cell recognition falls dramatically, concomitant with a reductions in transporter associated with antigen processing (TAP) function and surface human histocompatibility leukocyte antigen (HLA) class I expression. Screening of genes that are unique to EBV and closely related γ1-herpesviruses of Old World primates identified an early EBV lytic cycle gene, BNLF2a, which efficiently blocks antigen-specific CD8+ T cell recognition through HLA-A–, HLA-B–, and HLA-C–restricting alleles when expressed in target cells in vitro. The small (60–amino acid) BNLF2a protein mediated its effects through interacting with the TAP complex and inhibiting both its peptide- and ATP-binding functions. Furthermore, this targeting of the major histocompatibility complex class I pathway appears to be conserved among the BNLF2a homologues of Old World primate γ1-herpesviruses. Thus, even the acquisition of latent cycle genes endowing unique growth-transforming ability has not liberated these agents from evolutionary pressure to evade CD8+ T cell control over virus replicative foci

Thermochronology of the modern Indus River bedload: New insight into the controls on the marine stratigraphic record

The Indus River is the only major drainage in the western Himalaya and delivers a long geological record of continental erosion to the Arabian Sea, which may be deciphered and used to reconstruct orogenic growth if the modern bedload can be related to the mountains. In this study we collected thermochronologic data from river sediment collected near the modern delta. U-Pb ages of zircons spanning 3 Gyr show that only ∼5% of the eroding crust has been generated since India-Asia collision. The Greater Himalaya are the major source of zircons, with additional contributions from the Karakoram and Lesser Himalaya. The 39Ar/40Ar dating of muscovites gives ages that cluster between 10 and 25 Ma, differing from those recorded in the Bengal Fan. Biotite ages are generally younger, ranging 0–15 Ma. Modern average exhumation rates are estimated at ∼0.6 km/m.y. or less, and have slowed progressively since the early Miocene (∼20 Ma), although fission track (FT) dating of apatites may indicate a recent moderate acceleration in rates since the Pliocene (∼1.0 km/m.y.) driven by climate change. The 39Ar/40Ar and FT techniques emphasize the dominance of high topography in controlling the erosional flux to the ocean. Localized regions of tectonically driven, very rapid exhumation (e.g., Nanga Parbat, S. Karakoram metamorphic domes) do not dominate the erosional record

Omics analysis of educated platelets in cancer and benign disease of the pancreas

Pancreatic ductal adenocarcinoma (PDAC) is traditionally associated with thrombocy-tosis/hypercoagulation and novel insights on platelet-PDAC “dangerous liaisons” are warranted. Here we performed an integrative omics study investigating the biological processes of mRNAs and expressed miRNAs, as well as proteins in PDAC blood platelets, using benign disease as a refer-ence for inflammatory noise. Gene ontology mining revealed enrichment of RNA splicing, mRNA processing and translation initiation in miRNAs and proteins but depletion in RNA transcripts. Remarkably, correlation analyses revealed a negative regulation on SPARC transcription by isomiRs involved in cancer signaling, suggesting a specific ”education” in PDAC platelets. Platelets of benign patients were enriched for non-templated additions of G nucleotides (#ntaG) miRNAs, while PDAC presented length variation on 3′ (lv3p) as the most frequent modification on miRNAs. Additionally, we provided an actionable repertoire of PDAC and benign platelet-ome to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in patients with PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can “educate” the platelet. These novel findings could be further exploited for innovative liquid biopsies platforms as well as possible therapeutic targets